User:Karl Oberholser/Sandbox 3

Be patient, some green links have a delay before the structure is loaded! Examples from the PYL/PYR Family 

Introduction


The 3D structure of abscisic acid (ABA), a plant growth hormone, (default scene ) is shown in the applet without hydrogens. Abscisic acid binds to a family of proteins - pyrabactin resistance (PYR), PYR-like (PYL) or regulatory components of ABA receptor (RCAR) - which have been found to be involved in ABA signalling, and the structures of some family members have been determined. The structures of some of these receptors have bound ABA as well as a bound member of a type 2C protein phosphatase (PP2C) family.

Abscisic acid bound to PYR1 dimer
Abscisic acid bound to subunit B of the homodimeric receptor. Evidence indicates that the dimeric PYR1 is the biological unit even in the absence of ABA. Subunit A does not contain ABA, but water is in the ABA binding pocket.

Inter-dimer attractive forces: Several of the important interactions are cluster of four Phe which are part of the large α-helix,a Leu and a Pro, a hydrogen bond between Arg (blue N on side chain) in subunit B and Leu (red oxygen carbonyl) in subunit A and a Leu pair lower on the α-helix, also scene shows all of the above residues in spacefill. All of these residues overlaid with computed surface of open pockets. The pockets are joined in one continuous surface with the surfaces of the two subunits being fully connected in the area below the inter-dimer attractions. Dimer in spacefill overlaid with surface pockets.

Conformation differences due to ABA binding: ABA or water buried in the ABA binding sites formed by the surface pockets. Red spheres (water molecules) on the left are in the ABA binding site of subunit A, and red and gray atoms on the right are part of ABA bound to subunit B. Simplify view by showing only the pockets of the two ABA binding sites. Rotate the structure to observe that the site binding water is open to the surface, but the ABA binding site is not. Surface superimposed on the spacefilled display of the protein more clearly shows that the bound ABA is completely covered by the protein, but the water can be seen in the other subunit since the residues have not moved in subunit A as in B.



One aspect of the change in conformation is the movement of the "Pro-Cap" sequence in B subunit (green) but not in A subunit; this sequence in both subunits are seen here in spacefill. <scene name='User:Karl_Oberholser/Sandbox_3/Pockets_pro_cap_sf/1'>(Default scene of second applet) Pro-Cap sequence of subunit B has moved over top of the ABA site, but the binding site (presented as a surface ) in A is completely exposed. With ABA binding the <scene name='User:Karl_Oberholser/Sandbox_3/Pockets_pro_cap_pivote/5'>Pro-Cap sequence pivotes between Ile 84 and Asn 90 of the B subunit and covers the ABA. An important component of this movement is the <scene name='User:Karl_Oberholser/Sandbox_3/Pockets_pro_cap_pro/3'>cis-to-trans isomerization of Pro88. This change in Pro moves the positions of the Leu87 and Ala89 side chains which along with the Pro are seen in ball & stick. Compare the positions of these residues of B subunit with the positions of the corresponding residues in A in the next scene which has the structure <scene name='User:Karl_Oberholser/Sandbox_3/Pockets_pro_cap_pro_rotated/1'>rotated 180 deg. Movement of the <scene name='User:Karl_Oberholser/Sandbox_3/Pockets_leu_lock/2'>"Leu-Lock" sequence ( Glu114 - Thr118 ) secures the ABA. Notice that Arg116 extends toward the A subunit and hydrogen bonds with the Leu carbonyl in Pro-Cap sequence of A.

Another way of viewing these differences in conformation is to align two structures containing the different conformations. <scene name='User:Karl_Oberholser/Sandbox_3/3k3k3kay/8'>Show dimeric PYR1 binding ABA (red) aligned with dimeric PYL1 not binding ABA (blue) Observe that the secondary and tertiary structures are much the same, but some parts of the structure are better aligned than others. When the two models are <scene name='User:Karl_Oberholser/Sandbox_3/3k3k3kay_anim/3'>alternately displayed, it appears that PYR1 is more compact than PYL1. <scene name='User:Karl_Oberholser/Sandbox_3/3k3k3kay_3models/3'>Show the above two structures alternating with ABA shown with PYL1, even though it is not bound to it, as well as PYR1. Observe that a loop and β-strand comes over the top of ABA in PYR1 in ways that it does not in PYL1. Water in the ABA binding sites of the A subunits is also being displayed. <scene name='User:Karl_Oberholser/Sandbox_3/3k3k3kay_3models_pro_cap/2'>Compare positions of 'Pro-Cap', also called 'Gate', sequences. As seen in B subunit of PYR1 which binds ABA, this sequence of amino acids moves to cover ABA, but with the PYR1 A subunit and the two subunits of PYL1 which do not bind ABA the sequence does not move. <scene name='User:Karl_Oberholser/Sandbox_3/3k3k3kay_3models_leu_lock/1'>Compare positions of 'Leu-Lock' <applet load='3k3k3kay' size='400' frame='true' align='right' caption='3k3k3kay' scene='User:Karl_Oberholser/Sandbox_3/3k3k3kay_3models/3' />

isosurface minset 1000 ignore (A8S or HOH) POCKET cavity 1.0 sasurface 0.2 expanded residues: 59, 83, 88, 89, 92, 108, 110, 117, 120, 159, 163, 83-90, 114-118, 147-159 "../images/c/c4/Expand_residues.jvxl"

two smaller pockets: 59, 83, 88, 89, 92, 108, 110, 117, 120, 159, 163 "../images/3/39/Two_binding_pockets.jvxl"

Notes and References
<applet load='3kb0' size='400' frame='true' align='right' caption='PYR1 with ABA' />

<applet load='3kay' size='400' frame='true' align='right' caption='Dimeric PYR1' />

<applet load='3kaz' size='400' frame='true' align='right' caption='Trimeric PYR1 with butandiol' />

<applet load='3kb3' size='400' frame='true' align='right' caption='PYR1 with phosphatase' />